STRONG: metagenomics strain resolution on ...
Document type :
Article dans une revue scientifique
Title :
STRONG: metagenomics strain resolution on assembly graphs
Author(s) :
Limasset, Antoine [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Quince, Christopher [Auteur]
Nurk, Sergey [Auteur]
Raguideau, Sebastien [Auteur]
James, Robert [Auteur]
Soyer, Orkun [Auteur]
Summers, J. Kimberly [Auteur]
Eren, A. Murat [Auteur]
Chikhi, Rayan [Auteur]
Darling, Aaron [Auteur]

Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Quince, Christopher [Auteur]
Nurk, Sergey [Auteur]
Raguideau, Sebastien [Auteur]
James, Robert [Auteur]
Soyer, Orkun [Auteur]
Summers, J. Kimberly [Auteur]
Eren, A. Murat [Auteur]
Chikhi, Rayan [Auteur]

Darling, Aaron [Auteur]
Journal title :
Genome Biology
Publisher :
BioMed Central
Publication date :
2021-06-29
ISSN :
1465-6906
HAL domain(s) :
Informatique [cs]/Bio-informatique [q-bio.QM]
English abstract : [en]
Abstract We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and ...
Show more >Abstract We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.Show less >
Show more >Abstract We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.Show less >
Language :
Anglais
Peer reviewed article :
Oui
Audience :
Internationale
Popular science :
Non
Collections :
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